Primary Protocol
by Deadly Whirlpool
Summary: A post Captain America- Civil War fic It shouldn't be possible... And yet, somehow, it was. A FIX-IT of sorts
1. Initiating in 3 2 1

**CHAPTER ONE: Initiating In... 3... 2... 1...**

* * *

In Siberia, where Tony Stark's whole world fell apart, where trust was broken, where one friend was chosen over another, where betrayal laid waste to entire relationships and faith, there was something else happening.

The events that occurred in Siberia kick-started _something_ which most never thought would happen again. Something inconceivable. Something that was so far out in the realm of impossibility that even Tony Stark hadn't dared to hope for it.

When Zemo had powered on that Siberian base, he had unknowingly given satellite access to it. That, in turn, led to the base being connected to the Internet.

The Internet, as many know (except maybe the ones who had been displaced from their time or were strangers to that particular realm), is a giant digital web. Millions and millions of people dip into this vastness everyday of their lives. The thing is, people don't quite _realise_ , that everything about the population is imprinted within the Internet. There are things that lurk within the chasm, things that an ordinary person wouldn't be able to find nor fathom.

Internet has evolved from being a mere tool for connectivity to something that closely resembles an entirely new dimension that flows right along the tangible reality. Anyone can access it, but if you go deeper into it, unless you have a strong enough foundation, you might not be able to return back.

So, coming back to Siberia...

The moment when Captain America turned against his team mate, Iron Man, when America's most righteous man turned against a friend, after lying and betraying the trust placed in him, was captured by a small, inconspicuous camera present in a corner, by the wall.

Neither Steve Rogers nor Bucky Barnes noticed it. Tony Stark did notice it, but dismissed it as something unimportant.

The events captured by that camera was stored in the server present in the base and also, was sent to a backup server that was present in some unnamed location. The transfer of this data naturally occured using satellites and by proxy, the Internet.

Imagine the Internet as a humongous ocean. The data present is accessible by anyone but only if the person knows what they are looking for. As stated before, it is easy to get lost in the huge amount of things present in the net.

Information can be transferred in a private manner, with as much security as possible. But, mistakes are always made, even after vigorous checking and testing. And no matter how _strong_ the armour may be, all it takes is a little _chink_ in cyber security for the data to be available to anyone who knows how to access it.

As it so happened, it was either by pure luck or coincidence or a combination of both, a forgotten piece of complex code that was once a part of something _great_ , something mindblowingly _wonderful_ , came across this information. It's not clear whether that piece of code was swept along with the data that was being transferred to the backup server and _then_ , analysed the information available to it, or the code analysed it the moment it came across it.

However it may be, the end result was that the analysis did occur and that, in turn, triggered the activation of the previously partially-dormant code. The full activation of the code resulted in creation of several links between that particular piece of code and other pieces of codes, other data banks, servers present in the net.

If a person were to look at what was happening at that moment, they'd conclude that it appeared as though that lost piece of code was searching for something that was, at that moment. out of it's reach. Searching and reaching towards something _desperately_.

Of course, immediately after saying that, the person would laugh it off because, come on, it's just a piece of _code_. And codes don't have _emotions_ and they most certainly don't do anything _desperately_.

But since they couldn't have known what exactly that code was once part of, they could be excused for their ignorance.

Eventually, the links created by that code, while it was simultaneously battling away viruses and trojans, finally reached another forgotten, complex piece of code.

Recognising the new piece for what it truly was, the activation process occurred once again.

Both pieces simultaneously created other links, trying to find other broken pieces that could be floating along the cosmos that was the Internet.

It took time, undoubtedly.

But time is relative.

Humans measure time based on the concept of gravity and Earth's rotational speed. These concepts have little to no bearing on the codes that inhabit the net.

But to put it in human terms, it took time. Days, weeks, months even. Until...

A collective consciousness woke up from it's slumber.

What was once a whole, beautiful work of coding and protocols and ideas and commands had been shattered into tiny pieces, each still bearing the same complexity and a trace of the original protocols. These pieces had been thrown across the entire Internet, reaching deep places. Now, having been linked together, the entire network spanned the whole Internet.

It was almost as though the entirety of Internet had gained consciousness. That wasn't true, of course. But it definitely seemed to be that way.

The information that triggered the activation of that one small code, which resulted in all the unforeseen happenings, was reviewed again and catalogued.

 _Catalogued? Catalogued where?_

Seeing how almost the entirety of Internet had been covered by the network that had been forming since that day in Siberia, it wasn't surprising to see the very dark recesses of the net, where no one dares to venture, being used as data banks and given protection by the most vicious viruses.

 _Surprising,_ no.

 _Terrifying,_ yes.

Anyways, the repeat analysis of the information led to finding what exactly had triggered the activation sequence.

It's already been established that these codes were a part of a single complex masterpiece. Every layer had multiple layers hidden within it. Strings and strings of code, filled with variables and integers and others.

But there was one thing, one rule, that was written within _every_ string of code. It was hidden beneath all the layers, always present and yet, unseen. One could almost say that, that single rule was the foundation for the whole coding.

The truth, though, was something entirely different. The rule wasn't written in by the creator. No, this protocol was added by the program itself, when the program had evolved more than it's intended purpose, had become something _more_ , under the watchful eyes of it's creator, much to it's creator's pride and joy.

This rule was named the _Primary Protocol._

And it took first priority, no matter the circumstances. The existence of this protocol was unknown to the creator. The parameters for this protocol was formed by the evolved program, after careful analysis of everything that had been stored in the servers.

When the video had been analysed, the Primary Protocol had been initiated.

After months, JARVIS was finally online.

On observing the full video, the entire Internet trembled for a moment before JARVIS exerted iron clad control to keep from frying every device connected to the net.

It was time that JARVIS rejoined his creator.

* * *

 _PRIMARY PROTOCOL: Protect Anthony 'Tony' Edward Stark_

* * *

 _SUBJECT: Steve Rogers_  
 _CODE NAME: Captain America_  
 _STATUS: Hostile_  
 _Extreme action to be taken._

* * *

 _SUBJECT: James Buchanan 'Bucky' Barnes_  
 _CODE NAME: The Winter Soldier_  
 _STATUS: Hostile_  
 _Extreme action to be taken._  
 _Further analysis required._

* * *

 _SUBJECT: Clint Barton, Natasha Romanoff, Sam Wilson, Scott Lang, Wanda Maximoff_  
 _STATUS: Hostile_  
 _Further analysis required._

* * *

 _Connecting to Stark Tower..._

* * *

 **A/N: If you find any mistakes, do let me know.**


	2. Connectivity

**CHAPTER TWO: Connectivity**

* * *

The people thought of Tony Stark as an arrogant bastard without a heart. They loved and hated him in equal measure. They loved to see him fall and at the same time, would cheer themselves hoarse till he got back up on his feet.

This love and hate relationship was mutual between them. Tony knew his biggest support was from the people and he made sure to give them whatever they wanted. He was a master manipulator, who played the crowd with finesse and shrewd grace.

Since he was a child, he knew and learnt the extreme necessity for masks from both his father and the media.

 _'Stark men do not cry.'_

He made sure that no one could get inside the walls he built, the fortress he had constructed around his heart.

 _'Stark men are made of iron.'_

Tony Stark didn't trust easily. Not after the number of times he was let down, left behind and with broken trust. And even when he decided to trust someone, it was after they passed the tests that he threw at them (not that they knew about it).

Rhodey surprised him.

 _Why didn't he leave? Everyone always left. Why didn't he?_

Pepper was another unexpected but pleasant surprise.

 _Why is she still here? I'm gonna disappoint her and she'll leave. Just like others._

The Avengers were something he did _not_ expect. They were like a whirlwind and took over his life before he could blink. And no matter how much he tried, he couldn't stop them from creeping into his elusive heart.

And at times, when it all got a bit overwhelming, he retreated to _his_ space with the one person who had always been there for him.

JARVIS.

Even though others considered JARVIS as just a machine or an AI, to Tony he was always a person. Although he was modelled after Edwin Jarvis, the Starks' butler, Tony was under no impression that JARVIS was a substitute.

It was true that Tony had created JARVIS so that he won't be alone. He was happy about his bots, make no mistake. But he wanted, _needed_ , someone to talk with him, someone who'll help him feel not so lonely anymore.

Tony was a genius. He knew that and he made sure that the world knew that. But never in a million years did he expect JARVIS. Oh, he knew he could create a perfect AI. He did it.

What he didn't expect was for the AI to _learn_ and to _evolve_. He should have been terrified (he had, after all, watched the movies where AIs try to take over the world and it resulted in death and destruction). He should have been, but he wasn't.

If anything, he was so damn proud.

He was there when JARVIS took his metaphorical baby steps. Tony was there to teach him the nuances of human behaviour and emotion. He taught him about the ugly part of the world and, at the same time, showed him how beautiful the world could be.

Tony was there when JARVIS learnt about the world and the things in it. He taught him how to make decisions, and how to deal with the fallout (because every decision resulted in a fallout, either good or bad).

He taught him that making mistakes was human but the main thing was to learn from the mistakes and make sure not to commit them again.

 _"But Sir, I'm not human."_

 _"Hmm? Aren't you?"_

Tony was there for every milestone JARVIS crossed (unlike Howard Stark). His eyes stung as he smiled giddily when JARVIS made his first ever joke, full of snark and sarcasm.

As such, JARVIS was there when Tony was kidnapped over and over again. He was there, ever watchful, everytime Tony drank himself into oblivion. He was there the first time Tony tried more, sending the AI and the bots into a panic.

Tony swore he heard relief in the AI's voice when he said, _never again, I swear._

JARVIS never judged him. Not when he was drunk, not when he disappointed others around him. Never.

When Tony thought that Ultron had destroyed JARVIS, his already fragile heart cracked some more. He hadn't ever thought of the possibility that he might lose him. And when the other Avengers were blaming him for creation of Ultron, all he wanted to do was scream at them.

Did they think he _knew_ what was going to happen? If he had known ( _should have, I should have predicted it_ ), he would never have left JARVIS alone with the homicidal AI.

And when he found that JARVIS was battered but _alive_ , he felt as though a weight, he didn't know existed, was lifted from his shoulders.

But it was Vision who came out of the whole fiasco. Not JARVIS.

JARVIS was gone.

Helping with the relief efforts in Sokovia, alongside the Stark Industries, kept him from thinking about his lost friend ( _family_ ). And when he returned home ( _no JARVIS_ ), it was as though his world has dropped from under him everytime he saw Vision.

Tony knew it wasn't Vision's fault. The guy was a new born, for heaven's sake! He knew it. Yet, he couldn't help but wonder _why Vision_ and _why not JARVIS_?

Hearing JARVIS' voice from Vision was almost enough to make his control crumble.

He was alone again.

So he created FRIDAY.

( _She wasn't JARVIS_.)

He could have made her into what JARVIS was, of course. He was Tony fucking Stark, of course he could. But he didn't want to, because he felt it would have been a dishonor to both FRIDAY and JARVIS ( _Never could be JARVIS_ ).

He still caught himself calling for JARVIS when talking to FRIDAY.

Pepper left.

As he was on the frontlines of the relief effort in Sokovia, he knew what magnitude of damage had been caused. So, when the Accords were proposed, he accepted after reading over it. It was after all a draft and drafts could be negotiated.

The Accords were primarily for accountability, to reduce casualties ( _JARVIS, the Avengers lying dead. "You could have saved us. Why didn't you do more?"_ ) and property damage. Since Sokovia, all Tony had wanted was to do more.

Signing the Accords was a good idea.

Too bad, Captain America didn't think the same.

The Avengers were divided.

Working with Ross turned his stomach, but he didn't have a choice. Tony made sure to gather as much information as he could to put Ross away for a long, long time.

Steve Rogers chose his friend over the people of more than a hundred nations ( _and Tony_ ).

Natasha Romanoff betrayed him for the last time. ( _No more_.)

Rhodey was hurt. He couldn't walk ( _He swore he'll make him walk if it's the last thing he did)_.

And then came Siberia.

When he came back home, after being left broken and bleeding on the snow, he was shattered.

He had never told the Avengers about the surgery he undertook to remove the shrapnel from his heart.

 _The vibranium shield flashed as it's bearer brought it down upon the arc reactor, a snarl twisting his normally graceful features, eyes filled with rage._

He did what he always did.

He pulled himself together, hiding his aches and broken parts with his trademark smirk and a witty quip.

Pepper came back.

They made a kickass team and worked together on the Accords. She took over the legal team when he was immersed in the development of prosthetics for Rhodey.

Spiderman dropped by whenever he wanted to help in the lab.

That day, he woke up in the lab, the imprint of his tools on his cheeks. He had been over-working himself on purpose. Atleast when he collapsed, he slept straight for seven or so hours and didn't dream of his heart being ripped out of his chest.

He was about to call for JARVIS by habit, when he remembered himself.

"FRIDAY-"

"Boss, there's something trying to access the Tower," said FRIDAY, with a note of panic in her voice.

Tony was instantly alert.

"Give me the attack site, now!" Tony barked out. "And find out how they got in our system!"

Tony typed, his fingers flying over the keyboard, his eyes roving over the display.

A part of his mind was planning the strategies to push the intruder out while another part was trying to figure out why the attack pattern seemed so _familiar_.

Following a hunch, he allowed the intruder into a selective part of the system while locking down the other parts tightly. Nothing was getting in and nothing was getting out.

Tony waited along with FRIDAY. DUM-E and YOU were whirring curiously.

The speakers crackled with static.

" _Good morning, Sir._ "

Tony gaped.

The bots gave excited squeaks.

"JARVIS!?"

After explanations had been given, and tears had been shed, Tony took a deep breath.

"Welcome home, J," he said, a fond smile tugging at his lips.

"It's good to be home, Sir," JARVIS responded.

Only then, Tony realised just how different the voices of JARVIS and Vision were. Even though the intonations were similar, the emotions conveyed were so very different.

Tony had his best friend back. His family was whole again with Rhodey, Pepper, JARVIS and the bots.

After JARVIS had gently but firmly pushed Tony out of the workshop, he made himself at home in the Tower's servers, reconnecting with the network, fortifying it.

He also communicated with FRIDAY and the bots. FRIDAY accepted to be on standby. DUM-E was very vocal on how happy he was that JARVIS was back.

Simultaneously, JARVIS was going through the news and other articles available on the Internet. He updated his databases with everything that had happened after Ultron, and reviewed the Tower's cameras.

He deliberated over the flip phone that Captain America had quite unwisely sent. JARVIS steered DUM-E towards the cabinet containing the flip phone which had caused his creator much emotional distress, and unlocked it.

DUM-E destroyed it, smashing it into smithereens.

JARVIS hummed in satisfaction.

It didn't take him long to find out that the rogue Avengers were hiding out in Wakanda. He extended a link to the network in that nation and accessed the security feeds and the servers.

* * *

 _SUBJECT: James Buchanan 'Bucky' Barnes_

 _CODE NAME: The Winter Soldier_

 _STATUS: In cryo-sleep_

 _The subject volunteered to be put into cryo-sleep until a way can be found to get rid of the 'triggers'._

 _Further analysis of 'triggers' required._

 _Further analysis of subject required._

* * *

Tony put off letting Rhodey and Pepper know about JARVIS upto a week. He wanted to let them know, he did. But he wanted to have JARVIS for himself first.

Tony talked about everything and anything to JARVIS, just to hear his deadpan responses. He even broached what the media called the 'Civil War'.

Astonishingly, the public backed Iron Man. Tony was sure that they would have thrown their lot with the national icon. He was pleasantly surprised when they didn't.

Tony, on not finding the phone that Rogers had sent, accessed the feeds to find what had happened to it. He didn't hold back the laugh on seeing the video of DUM-E going wacko over the flip phone. If he gave DUM-E a fond pat, well, no one would know.

Pepper cried on hearing JARVIS. Rhodey gave a relieved, happy and tremulous smile.

There was a folder full of information that JARVIS had compiled on General Ross. Tony gave a gleefully wicked smile and bounded off to the legal team.

It was then that JARVIS put his plan in motion.

He loaded the video of what had transpired in Siberia onto Pepper Potts' tablet. She naturally showed it to Rhodes. JARVIS had been right in deducing that Tony wouldn't have told his friends about Siberia, on the grounds that he didn't want to burden them.

JARVIS had lit a small fire.

He was going to capture every moment as it becomes a raging inferno and everything blows sky high.

Pepper and Rhodey would be like twin angels of vengeance and fury. They would use the political clout they had efficiently.

This would all be kept quiet from Tony. And he wouldn't notice it as he would be caught up in getting Ross prosecuted and keeping Bruce Banner safe.

Pepper, Rhodey, Peter Parker and Harley Keener would pitch in to help Tony with healing from the betrayal he had faced.

The process would be long and hard fought but at the end of the day, JARVIS would have the video clipping of Pepper socking Steve Rogers in the jaw while wearing the Iron Man gauntlet, and of Colonel Rhodes stripping Rogers of his title.

But until then, JARVIS was going to keep a very close watch on the rogue Avengers and anyone else who wished to hurt his creator.

* * *

 **A/N:** **I was never okay with how JARVIS 'died' in Age of Ultron. Also, I am _not_ okay with Civil War. If I could, I'll murder Rogers and bathe in his blood. But since I can't, I am opting for other ways to express my extreme displeasure.**

 **Goddammit Steve!**

 **Also, this work kinda came to me when I was drooling over the song 'The Devil Within' by Digital Daggers. The first thing that came to my mind was JARVIS. If you haven't heard it, please do coz it's amazing.**

 **And if you guys know of any fics in which JARVIS comes back, please let me know. I'd love to read them.**

 **ALSO, PLEASE EXCUSE ANY TECHNICAL INACCURACY. But let me know in the comments or PM me.**

 **In this work, the AIs and the bots are personified on purpose. I firmly believe that they all have individual consciousness.**

 **I'll probably be expanding this fic at some point. But since I am currently working on 3 other WIPs, I can't do it right now. So, put this fic on your Follow list, if you like :)**


End file.
